AMBER Archive (2009)

Subject: [AMBER] Fwd: AMBER: MM-PBSA in AMBER 10

From: Daniel Oehme (oehmes4_at_gmail.com)
Date: Thu Mar 26 2009 - 18:44:59 CDT

Hi all,

Recently I have been getting some direct emails in relation to the
modifications I made to the perl scripts for MM-PBSA in relation to
the error I was getting for the "No data for 0+0 PB ELRAELE 0" error.
I did get some feedback from Dr Gohlke's lab stating that
modifications I made are acceptable.

Also in their response it was mentioned that they would make some
changes to the examples and the mm_pbsa_statistics script as soon as
possible to clear up these issues. I am not sure if this is happening
but I thought I would let everyone know that they can edit the files
themselves and get MM-PBSA in AMBER 10 to run properly.

Daniel Oehme
PhD student
La Trobe University

On Mon, Jun 23, 2008 at 4:07 PM, Daniel Oehme <oehmes4_at_gmail.com> wrote:
> Hi,
>
> I have recently received a copy of AMBER 10 and have been running some
> tests with the MM-PBSA suite of perl scripts. I have come across a
> couple of issues while doing so.
>
> The first is that the mm_pbsa.in files in the Examples directory have
> the the AMBER9 format not AMBER10. The mm_pbsa.in in
> $AMBERHOME/src/mm_pbsa/Examples is correct but the ones in the
> 01_GenerateSnapshots, 03_MMPBSA_Binding etc are of the old format.
>
> Secondly, running the ras_raf 03_MMPBSA_Binding example did not work,
> even when changes were made to mm_pbsa.in to align it with the AMBER10
> format. The error I got was "No data for 0+0 PB ELRAELE 0". By
> searching the perl scripts I was able find ELRAELE defined in
> mm_pbsa_statistics.pm. I edited mm_pbsa_statistics.pm. such that the
> $PB section of $VARREG (Lines 131-143) read:
>         "PB" => {
>                   "ELRAELE"  => [0,0,'ELRAELE = +(-?\d+\.\d+)'], #
>                   "EPB"      => [0,0,'EPB = +(-?\d+\.\d+)'],
>                   "PB"       => [1,0,'corrected reaction field
> energy: +(-?\d+\.\d+)'],
>                   "PBDIS"    => [1,0,'EDISPER = +(-?\d+\.\d+)'],
>                   "PBCAV"    => [1,0,'ECAVITY = +(\d+\.\d+)'],
>                   "PBNONPOL" => [0,0,'ENPOLAR = +(\d+\.\d+)'],
>                   "PBSUR"    => [3,5],
>                   "PBCAL"    => [3,6],
>                   "PBSOL"    => [2,7,'+PB_PBCAL+PB_PBSUR+PB_PBDIS'],
>                   "PBELE"    => [2,8,'+PB_PBCAL+?MM_ELE'],
>                   "PBTOT"    => [2,9,'+PB_PBSOL+?MM_GAS']
>                 },
> By changing index 0 of ELRAELE, EPB, PBNONPOL to 0, MM-PBSA would
> complete. Can anyone tell me if this was a valid way of solving the
> problem or have I misunderstood something.
>
> Finally, reading though the changes to mm_pbsa.in I noticed that the
> Surften and Surfoff values have been changed from the values used in
> AMBER9, to values which depend on the radii type used or if IVCAP is
> set. My questions regarding this are first - have the values that have
> been suggested for Surften/Surfoff been published anywhere. Secondly,
> why are the AMBER9 values used for Surften and Surfoff in the GB
> calculations section instead of the new values as given in the PB
> section. I would think that the non polar solvation energy would be
> independent of the implicit solvent method used and therefore the same
> value for Surften/Surfoff should be used for both methods
>
> Thanks in advance for any help I receive.
>
> Daniel Oehme
> PhD student
> La Trobe University
>

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